Homology modeling and docking studies of IscS from extremophile Acidithiobacillus ferrooxidans

Abstract

The gene iscS-3 from Acidithiobacillus ferrooxidans may play a central role in the delivery of sulfur to a variety of metabolic pathways in this organism. For insight into the sulfur metabolic mechanism of the bacteria, an integral three-dimensional (3D) molecular structure of the protein encoded by this gene was built by homology modeling techniques, refined by molecular dynamics simulations, assessed by PROFILE-3D and PROSTAT programs and further used to search bind sites, carry out flexible docking with cofactor pyridoxal 5′-phosphate(PLP) and substrate cysteine and hereby detect its key residues. Through these procedures, the detail conformations of PLP-IscS(P-I) and cysteine-PLP-IscS(C-P-I) complexes were obtained. In P-I complex, the residues of Lys208, His106, Thr78, Ser205, His207, Asp182 and Gln185 have large interaction energies and/or hydrogen bonds fixation with PLP. In C-P-I complex, the amino group in cysteine is very near His106, Lys208 and PLP, the interaction energies for cysteine with them are very high. The above results are well consistent with those experimental facts of the homologues from other sources. Interestingly, the four residues of Glu105, Glu79, Ser203 and His180 in P-I docking and the residue of Lys213 in C-P-I docking also have great interaction energies, which are fitly conservation in IscSs from all kinds of sources but have not been identified before. From these results, this gene can be confirmed at 3D level to encode the iron-sulfur cluster assembly protein IscS and subsequently play a sulfur traffic role. Furthermore, the substrate cysteine can be presumed to be effectively recruited into the active site. Finally, the above detected key residues can be conjectured to be directly responsible for the bind and/or catalysis of PLP and cysteine.

Keywords

bioleaching / IscS / Acidithiobacillus ferrooxidans / homology modeling / molecular dynamics / docking / pyridoxal 5′-phosphate(PLP) / cysteine

References

[1] RawlingsD. E., KusanoT.. Molecular genetics of Thiobacillus ferrooxidans[J]. Microbiological Reviews, 1994, 58(1): 39-55

[2] BakerB. J., BanfieldJ. F.. Microbial communities in acid mine drainage[J]. FEMS Microbiology Ecology, 2003, 44(2): 139-152

[3] TuovinenO. H., NiemelaS. I., GyllenbergH. G.. Tolerance of Thiobacillus ferrooxidations to some metals[J]. Antonie Van Leeuwenhoek, 1971, 37(4): 489-496

[4] BanerjeeP. C.. Genetics of metal resistance in acidophilic prokaryotes of acidic mine environments[J]. Indian Journal of Experimental Biology, 2004, 42(1): 9-25

[5] QuatriniR., Appia-AymeC., DenisY., et al.. Insights into the iron and sulfur energetic metabolism of Acidithiobacillus ferrooxidans by microarray transcriptome profiling[J]. Hydrometallurgy, 2006, 83(1/4): 263-272

[6] MiharaH., EsakiN.. Bacterial cysteine desulfurases: Their function and mechanisms[J]. Applied Microbiology and Biotechnology, 2002, 60(1/2): 12-23

[7] JohnsonD. C., DeanD. R., SmithA. D., et al.. Structure, function, and formation of biological iron-sulfur clusters[J]. Annual Review of Biochemistry, 2005, 74: 247-281

[8] UrbinaH. D., SilbergJ. J., HoffK. G., et al.. Transfer of sulfur from IscS to IscU during Fe-S cluster assembly[J]. Journal of Biological Chemistry, 2001, 276(48): 44521-44526

[9] LauhonC. T.. Requirement for IscS in biosynthesis of all thionucleosides in Escherichia coli[J]. Journal of Bacteriology, 2002, 184(24): 6820-6829

[10] BuiB. T. S., EscalettesB., ChottardF., et al.. Enzyme-mediated sulfide production for the reconstitution of [2Fe-2S] clusters into apo-biotin synthase of Escherichia coli[J]. European Journal of Biochemistry, 2000, 267(9): 2688-2694

[11] Cupp-VickeryJ. R., UrbinaH., VickeryL. E.. Crystal structure of IscS — A cysteine desulfurase from Escherichia coli[J]. Journal of Molecular Biology, 2003, 330(5): 1049-1059

[12] KaiserJ. T., ClausenT., BourenkowG. P., et al.. Crystal structure of a NifS-like protein from Thermotoga maritima: Implications for iron sulphur cluster assembly[J]. Journal of Molecular Biology, 2000, 297(2): 451-464

[13] BlundellT. L., SibandaB. L., SternbergM. J. E., et al.. Knowledge-based prediction of protein structures and the design of novel molecules[J]. Nature, 1987, 326(6111): 347-352

[14] LipmanD. J., PearsonW. R.. Rapid and sensitive protein similarity searches[J]. Science, 1985, 227(4693): 1435-1441

[15] SaliA., PottertonL., YuanF., et al.. Evaluation of comparative protein modeling by MODELLER[J]. Proteins, 1995, 23(3): 318-326

[16] PonderJ. W., RichardsF. M.. Tertiary templates for proteins: Use of packing criteria in the enumeration of allowed sequences for different structural classes[J]. Journal of Molecular Biology, 1987, 193(4): 775-791

[17] JorgensenW. L., ChandrasekharJ., MaduraJ. D., et al.. Comparison of simple potential functions for simulating liquid water[J]. Journal of Chemical Physics, 1983, 79(2): 926-935

[18] LuthyR., BowieJ. U., EisenbergD.. Assessment of protein models with three-dimensional profiles[J]. Nature, 1992, 356(6364): 83-85

[19] MorrisA. L., MacarthurM. W., HutchinsonE. G., et al.. Stereochemical quality of protein structure coordinates[J]. Proteins, 1992, 12(4): 345-364

[20] KuntzI. D., BlaneyJ. M., OatleyS. J., et al.. A geometric approach to macromolecule-ligand interactions[J]. Journal of Molecular Biology, 1982, 161(2): 269-288